When you indorse a check or stock certificate, you typically sign it on the back.  That makes etymological sense because "indorse" is derived from the Latin preposition in, meaning on, and dorsum, meaning back. 

But why do some folks choose to write "endorse" rather than "indorse"?  The prefix "en" is the French derivation of the Latin "in".  French made it into the English legal system as a result of the well-known visitation of William the Conquerer in 1066.  As a result, the "great and the good" in England were French speaking Normans. 

The drafters of the Uniform Commercial Code appear to have been undecided or simply striving for the elegance of variation because you can find both spellings throughout the Code.  For example, Section 3204 provides "'Indorsement' means a signature . . ." and Section 8201(a)(11) provides "'Endorsement' means a signature . . .".